modified:   uploadNeuroDB/bin/mincpik

mincpik has been changed to a newer version (the one in the CIVET quarantine)
	modified:   uploadNeuroDB/NeuroDB/MRI.pm
	modified:   uploadNeuroDB/tarchiveLoader

Include:
- Zia's protocol_violated code
- screening BOLD images using the time dimension
Link repair
	modified:   Mincinfo
	modified:   concat_mri.pl
	modified:   minc2jiv.pl
Merge branch 'to_merge'

Conflicts:
	uploadNeuroDB/NeuroDB/MRI.pm
	uploadNeuroDB/tarchiveLoader
Permission changes and fixed a PATH in copy_and_process_tarchive (to give the full path to tarchiveLoader while calling from cron scripts)
Merge remote-tracking branch 'aces/master'
Task conversion pipeline.
Removed comment lines.
	modified:   convertDCM2NII.pl
Fixed Task conversion pipeline
Removed copy_process_tarchive step from the MRI pipeline
Modified the tarchiveLoader so that once a minc has been identified, it moves the tarchive to a year subfolder and update the tarchive table.
Result: only one copy of the tarchive will be kept on the server.
Added an exit when tarchive does not exist.
Simplified a print.
Removed one of the two if statements that have been inserted by mistake.
Merge remote-tracking branch 'aces/master' into test_merge
Fixed a bug that prevailed SeriesUID to be inserted into the mri_protocol_violated_scan table.
Back up all pipeline scripts into GitHub
Merge remote-tracking branch 'aces/master' into testMergeLORIS

Conflicts:
	batch_uploads_tarchive
	environment
	uploadNeuroDB/tarchiveLoader

Merged Loris-MRI to master.
Added script to mass convert DICOM files to nifti according to INDI organisation
Merge branch 'DTI_QC_register' into MergeDTIPrep